Rationale: This script performs differential gene expression (dge) and calculates the upregulated and downregulated genes in different parts of lichen thallus using Sleuth
library(sleuth)
library(tidyverse)
samples<-read.delim("../data/metadata/found_samples_in_sequences_db_thallus.csv",sep=",")
kal_dirs2 <- data.frame("sample"=samples$run_id, "part"= samples$sample_focus,
substrate=samples$growth_site, thallus = samples$thallus_id,
"path"=paste0("../analysis_and_temp_files/06_meta_mapping/kallisto_meta_mapping/",samples$run_id,"_kallisto")) %>% filter(sample!="MP_I" & sample!="MP_II")
full<-read.delim("../analysis_and_temp_files/08_dge_culture_lichen/counts_table.tsv",row.names=1)
d<-full %>% select(any_of(kal_dirs2$sample)) #include only lichen samples
colnames(d)
## [1] "XBC2" "XBA1" "XSA2_2" "XSC1" "XSE2" "XBE1" "XTA2" "XSC2"
## [9] "XSA2" "XBA2" "XBC1" "XTA1" "XSA1" "XTC2" "XTE2" "XBE2"
## [17] "XMC2"
d$max<-apply(d,1,max)
min(d$max)
## [1] 0
d1<-d[which(d$max>=5),] #to remove lowly expressed genes, keep rows in which max read count across whole panel is atleast 5
# drop the max column, as its not needed anymore
raw_counts<-d1 %>% select(-max)
length(rownames(d1)) # total number of genes
## [1] 11083
length(rownames(raw_counts))
## [1] 11083
#make the list of selected genes
target_id<-rownames(d1)
ec_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "thallus_edge") )
ec_dirs$part <- as.factor(ec_dirs$part)
ec_so <- sleuth_prep(ec_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ..........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ..........
#model that includes only confounding variables
ec_so <- sleuth_fit(ec_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ec_so <- sleuth_fit(ec_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 7 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_000969-T1, XANPAGTX0501_000980-T1, XANPAGTX0501_002903-T1, XANPAGTX0501_004641-T1, XANPAGTX0501_005100-T1, XANPAGTX0501_006796-T1
## computing variance of betas
#compare the models
ec_so <- sleuth_lrt(ec_so, 'reduced', 'full')
ec_so <- sleuth_wt(ec_so, 'partthallus_edge')
plot_pca(ec_so, color_by = 'part', text_labels = TRUE,use_filtered=T)
ec_table <- sleuth_results(ec_so, 'partthallus_edge')
ec_sig <- ec_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "centre", "low_logFC")))
table(ec_sig$change)
##
## centre low_logFC
## 9 170
ec_dge<-ec_sig$target_id[ec_sig$change!="low_logFC"]
plot_bootstrap(ec_so,
target_id = ec_dge[7],
units = "est_counts",
color_by = "part")
plot_bootstrap(ec_so,
target_id = ec_dge[6],
units = "est_counts",
color_by = "part")
library(kableExtra)
funannot2<-read.delim2("../../02_long_read_assemblies/analysis_and_temp_files/09_ortho/lichen_enriched_ortho_in_xanpa.tsv",sep="\t")
center_ec_genes<-ec_sig %>% filter(change=="centre") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
center_ec_genes %>%
kable(format = "html", col.names = colnames(center_ec_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_005615-T1 | -1.009109 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005614-T1 | -1.075863 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008007-T1 | -1.155943 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002184-T1 | -1.173653 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001949-T1 | -1.187615 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002506-T1 | -1.194636 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008856-T1 | -1.278297 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009886-T1 | -1.292990 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009927-T1 | -1.619707 | NA | NA | NA | FALSE | TRUE |
plot_bootstrap(ec_so,
target_id = ec_sig$target_id[ec_sig$b>0.9],
units = "est_counts",
color_by = "part")
edge_ec_genes<-ec_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
edge_ec_genes %>%
kable(format = "html", col.names = colnames(edge_ec_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001015-T1 | 0.9022441 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | NA | NA | TRUE | FALSE |
ggplot(ec_table)+geom_histogram(aes(x=pval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).
library(MKpower)
qqunif(ec_table$pval, color.line = "orange")
ggplot(ec_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).
* Perhaps, this particular comparison is underpowered
library(MKpower)
qqunif(ec_table$qval, color.line = "orange")
ca_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_centre", "apothecia") )
ca_dirs$part <- as.factor(ca_dirs$part)
ca_dirs$thallus<- as.factor(ca_dirs$thallus)
rhdf5::h5closeAll()
ca_so <- sleuth_prep(ca_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .............
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .............
#model that includes only confounding variables
ca_so <- sleuth_fit(ca_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 2 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ca_so <- sleuth_fit(ca_so, ~thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 3 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_004237-T1, XANPAGTX0501_010518-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ca_so <- sleuth_lrt(ca_so, 'reduced', 'full')
ca_so <- sleuth_wt(ca_so, 'partthallus_centre')
plot_pca(ca_so, color_by = 'part', text_labels = TRUE,use_filtered=T)
ca_table <- sleuth_results(ca_so, 'partthallus_centre')
ca_sig <- ca_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "centre", ifelse(b< -1, "apothecium", "low_logFC")))
table(ca_sig$change)
##
## apothecium centre low_logFC
## 118 1 1928
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.min(ca_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.min(ca_sig$b[-which.min(ca_sig$b)])],
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "part")
ap_ca_genes<-ca_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ca_genes %>%
kable(format = "html", col.names = colnames(ap_ca_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_001605-T1 | -1.002217 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004628-T1 | -1.002890 | IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K03469 | FALSE | FALSE |
| XANPAGTX0501_009621-T1 | -1.004737 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008874-T1 | -1.005597 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007403-T1 | -1.005610 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004416-T1 | -1.006355 | IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 | NA | T02 | K08657 | FALSE | FALSE |
| XANPAGTX0501_009141-T1 | -1.008026 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002166-T1 | -1.010246 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003282-T1 | -1.010415 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006245-T1 | -1.011007 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_001082-T1 | -1.011584 | IPR004853 Sugar phosphate transporter domain | NA | NA | K26222 | FALSE | FALSE |
| XANPAGTX0501_002170-T1 | -1.014622 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002104-T1 | -1.017319 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002183-T1 | -1.017368 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004494-T1 | -1.018387 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007464-T1 | -1.021451 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005615-T1 | -1.022220 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001888-T1 | -1.023478 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005658-T1 | -1.031831 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002163-T1 | -1.035184 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008533-T1 | -1.037400 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009317-T1 | -1.039048 | IPR008979 Galactose-binding-like domain superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_005061-T1 | -1.045582 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001947-T1 | -1.046488 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004580-T1 | -1.050842 | IPR007292 Nuclear fusion protein Kar5 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006974-T1 | -1.052396 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002057-T1 | -1.052723 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006203-T1 | -1.055462 | IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002184-T1 | -1.055941 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001330-T1 | -1.062267 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004493-T1 | -1.069215 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005597-T1 | -1.070417 | IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain | GH133 | NA | K01196 | FALSE | FALSE |
| XANPAGTX0501_008628-T1 | -1.071911 | IPR023346 Lysozyme-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003775-T1 | -1.074091 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K11593 | FALSE | FALSE |
| XANPAGTX0501_000647-T1 | -1.082215 | IPR000571 Zinc finger, CCCH-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006255-T1 | -1.084624 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010303-T1 | -1.086556 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004891-T1 | -1.088838 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000681-T1 | -1.089087 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001010-T1 | -1.089790 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004217-T1 | -1.090288 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | K24990 | FALSE | FALSE |
| XANPAGTX0501_001436-T1 | -1.091349 | IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006910-T1 | -1.092752 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007871-T1 | -1.093262 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000005-T1 | -1.100476 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009139-T1 | -1.106326 | IPR001876 Zinc finger, RanBP2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001333-T1 | -1.109653 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003212-T1 | -1.110801 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008009-T1 | -1.110995 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006016-T1 | -1.111020 | IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal | GH63 | NA | FALSE | FALSE | |
| XANPAGTX0501_008008-T1 | -1.111120 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006330-T1 | -1.113100 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004104-T1 | -1.113445 | IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001362-T1 | -1.113981 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001951-T1 | -1.118810 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005630-T1 | -1.120143 | IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008534-T1 | -1.122508 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000025-T1 | -1.123779 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004950-T1 | -1.124212 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002522-T1 | -1.132906 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003572-T1 | -1.135075 | IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily | CE16 | NA | TRUE | FALSE | |
| XANPAGTX0501_007067-T1 | -1.135736 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007234-T1 | -1.142869 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007262-T1 | -1.143084 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010203-T1 | -1.143084 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005279-T1 | -1.148052 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010380-T1 | -1.148975 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010007-T1 | -1.149075 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009615-T1 | -1.156978 | IPR035940 CAP superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002172-T1 | -1.161670 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003209-T1 | -1.170208 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008041-T1 | -1.181328 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001910-T1 | -1.190522 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009318-T1 | -1.192876 | IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004521-T1 | -1.198724 | IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001612-T1 | -1.207043 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010304-T1 | -1.207964 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001538-T1 | -1.211841 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009602-T1 | -1.212068 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008007-T1 | -1.213991 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008782-T1 | -1.216240 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006951-T1 | -1.222177 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005402-T1 | -1.225284 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001414-T1 | -1.228686 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000194-T1 | -1.233329 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | K01176 | FALSE | FALSE |
| XANPAGTX0501_005766-T1 | -1.254576 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009582-T1 | -1.264645 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005735-T1 | -1.281286 | IPR018824 Conidiation-specific protein 6 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008331-T1 | -1.288651 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001611-T1 | -1.298257 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007900-T1 | -1.308741 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008090-T1 | -1.312749 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002182-T1 | -1.314625 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009619-T1 | -1.314627 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008284-T1 | -1.314835 | IPR029044 Nucleotide-diphospho-sugar transferases | GT2_Glyco_tranf_2 | NA | FALSE | FALSE | |
| XANPAGTX0501_004520-T1 | -1.321604 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001963-T1 | -1.324243 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001960-T1 | -1.329881 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000193-T1 | -1.344509 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | FALSE | FALSE | |
| XANPAGTX0501_001967-T1 | -1.356557 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001063-T1 | -1.359981 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001856-T1 | -1.377390 | IPR037176 Osmotin/thaumatin-like superfamily | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_002506-T1 | -1.384452 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006327-T1 | -1.392539 | IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007397-T1 | -1.396019 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007872-T1 | -1.413947 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010596-T1 | -1.414271 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008420-T1 | -1.415724 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000892-T1 | -1.427350 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000378-T1 | -1.444983 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003211-T1 | -1.502300 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010280-T1 | -1.533833 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005814-T1 | -1.541250 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009786-T1 | -1.554050 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009926-T1 | -1.646262 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004966-T1 | -1.664164 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008109-T1 | -2.657633 | IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain | NA | NA | K03800 | FALSE | FALSE |
| XANPAGTX0501_001156-T3 | -3.910405 | IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily | NA | NA | K11644 | FALSE | FALSE |
mult_list<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/multicellularity.txt")
#select genes that come from one of the categories of interest
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_selected<-ips_df %>% mutate(ID=gsub( " .*$", "", InterPro_new)) %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-c(InterPro_new,short_term))
## Joining with `by = join_by(ID)`
ko_cazy_selected<-funannot2 %>% select(TranscriptID,KO,CAZyme_new) %>%
pivot_longer(-TranscriptID,names_to = "Annotation",values_to = "ID") %>% inner_join(mult_list,relationship = "many-to-many") %>% select(-Annotation)
## Joining with `by = join_by(ID)`
mult_gene_table<-rbind(ips_selected,ko_cazy_selected)
mult_gene_table_ap<-mult_gene_table %>% inner_join(ca_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | ID | Annotation_type | Description | Function | Function_type | b |
|---|---|---|---|---|---|---|
| XANPAGTX0501_005597-T1 | IPR032788 | IPR | Glycogen debranching enzyme, central domain | Carbohydrate storage | Fungal multicellularity | -1.070417 |
| XANPAGTX0501_000647-T1 | IPR000571 | IPR | Zinc finger, CCCH-type | Cell division, proliferation and growth | Fungal multicellularity | -1.082215 |
| XANPAGTX0501_003775-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.074091 |
| XANPAGTX0501_004104-T1 | IPR001214 | IPR | SET domain | Cell division, proliferation and growth | Fungal multicellularity | -1.113445 |
| XANPAGTX0501_004628-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.002890 |
| XANPAGTX0501_005735-T1 | IPR018824 | IPR | Conidiation-specific protein 6 | Cell surface and cell wall proteins | Fungal multicellularity | -1.281286 |
| XANPAGTX0501_006327-T1 | IPR018466 | IPR | Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | Cell wall biosynthesis | Fungal multicellularity | -1.392539 |
| XANPAGTX0501_001856-T1 | IPR037176 | IPR | Osmotin/thaumatin-like superfamily | Cell wall remodeling | Fungal multicellularity | -1.377390 |
| XANPAGTX0501_003212-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.110801 |
| XANPAGTX0501_006203-T1 | IPR017907 | IPR | Zinc finger; RING-type; conserved site | Protein ubiquitination | Fungal multicellularity | -1.055462 |
| XANPAGTX0501_010380-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.148975 |
| XANPAGTX0501_004217-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.090288 |
| XANPAGTX0501_003775-T1 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.074091 |
| XANPAGTX0501_006203-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.055462 |
###make table with IPS annotations
ips_df <-funannot2 %>% select(TranscriptID,InterPro_new) %>%
mutate(InterPro_new = strsplit(InterPro_new, ", I")) %>%
unnest(InterPro_new) %>% mutate(InterPro_new=str_replace(InterPro_new,"^PR","IPR")) %>%
mutate(short_term = substr(InterPro_new, 1,40))
ips_data <- list(
term2protein = data.frame(
term = ips_df$InterPro_new,
gene = ips_df$TranscriptID
),
term2name = data.frame(
term = ips_df$InterPro_new,
name = ips_df$short_term
),
universe = unique(as.character(ips_df$TranscriptID))
)
###enrichment analysis
enrich<-clusterProfiler::enricher(ap_ca_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)
plot_bootstrap(ca_so,
target_id = ca_sig$target_id[which.max(ca_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ca_so,
target_id = "XANPAGTX0501_004633-T1",
units = "est_counts",
color_by = "part")
ce_ca_genes<-ca_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ce_ca_genes %>%
kable(format = "html", col.names = colnames(ce_ca_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_006303-T1 | 1.3084877 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004633-T1 | 0.9765075 | NA | NA | NA | FALSE | FALSE |
ggplot(ca_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).
library(MKpower)
qqunif(ca_table$qval, color.line = "orange")
ea_dirs<-kal_dirs2 %>% filter(part %in% c("thallus_edge", "apothecia") )
ea_dirs$part <- as.factor(ea_dirs$part)
ea_dirs$thallus<- as.factor(ea_dirs$thallus)
rhdf5::h5closeAll()
ea_so <- sleuth_prep(ea_dirs,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## ...........
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## ...........
#model that includes only confounding variables
ea_so <- sleuth_fit(ea_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
ea_so <- sleuth_fit(ea_so, ~ thallus + part, 'full')
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
ea_so <- sleuth_lrt(ea_so, 'reduced', 'full')
ea_so <- sleuth_wt(ea_so, 'partthallus_edge')
ea_table <- sleuth_results(ea_so, 'partthallus_edge')
ea_sig <- ea_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "edge", ifelse(b< -1, "apothecium", "low_logFC")))
plot_pca(ea_so, color_by = 'part', text_labels = TRUE,use_filtered=T)
table(ea_sig$change)
##
## apothecium edge low_logFC
## 371 13 1772
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.min(ea_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.min(ea_sig$b[-which.min(ea_sig$b)])],
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_002103-T1",
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_002104-T1",
units = "est_counts",
color_by = "part")
ap_ea_genes<-ea_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_ea_genes %>%
kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_006767-T1 | -1.001121 | IPR017956 AT hook, DNA-binding motif | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001647-T1 | -1.003441 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006026-T1 | -1.005997 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010639-T1 | -1.009995 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000350-T1 | -1.010205 | IPR003439 ABC transporter-like, ATP-binding domain, IPR003593 AAA+ ATPase domain, IPR013525 ABC-2 type transporter, IPR017871 ABC transporter-like, conserved site, IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | K05681 | FALSE | FALSE |
| XANPAGTX0501_005347-T1 | -1.010680 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004759-T1 | -1.011221 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006900-T1 | -1.012780 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009389-T1 | -1.014539 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007378-T1 | -1.016970 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005621-T1 | -1.020780 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010022-T1 | -1.023610 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009499-T1 | -1.023663 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006945-T1 | -1.030462 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000661-T1 | -1.032709 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006946-T1 | -1.037233 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002624-T1 | -1.038299 | IPR029058 Alpha/Beta hydrolase fold | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010094-T1 | -1.039693 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008594-T1 | -1.040188 | IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001497-T1 | -1.040517 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000203-T1 | -1.040557 | IPR001938 Thaumatin family, IPR037176 Osmotin/thaumatin-like superfamily | GH152 | NA | TRUE | FALSE | |
| XANPAGTX0501_010087-T1 | -1.040935 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003186-T1 | -1.041709 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010640-T1 | -1.042747 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004003-T1 | -1.043412 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000909-T1 | -1.050406 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002181-T1 | -1.050504 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010204-T1 | -1.051517 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006142-T1 | -1.056449 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_005447-T1 | -1.060382 | IPR024500 Domain of unknown function DUF3074 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004484-T1 | -1.063011 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000065-T1 | -1.064314 | IPR027921 NOP protein chaperone 1 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006920-T1 | -1.066060 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003265-T1 | -1.067945 | IPR007203 ORMDL family | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002152-T1 | -1.069475 | IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR040632 Sulfotransferase, S. mansonii-type | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003742-T1 | -1.069824 | IPR001509 NAD-dependent epimerase/dehydratase, IPR036291 NAD(P)-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006931-T1 | -1.072494 | IPR013087 Zinc finger C2H2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002657-T1 | -1.073491 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005924-T1 | -1.074455 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007353-T1 | -1.077217 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005583-T1 | -1.079779 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009580-T1 | -1.091993 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004141-T1 | -1.102317 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010231-T1 | -1.104490 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008637-T1 | -1.106264 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_000885-T1 | -1.108859 | IPR036305 RGS domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003865-T1 | -1.109235 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_000417-T1 | -1.109737 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005025-T1 | -1.115496 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000848-T1 | -1.115545 | IPR016137 RGS domain, IPR036305 RGS domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006384-T1 | -1.125655 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004308-T1 | -1.127582 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010011-T1 | -1.134493 | IPR036013 Band 7/SPFH domain superfamily | NA | NA | K07192 | FALSE | FALSE |
| XANPAGTX0501_005047-T1 | -1.135514 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002639-T1 | -1.136570 | IPR002740 EVE domain, IPR015947 PUA-like superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006342-T1 | -1.138964 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004244-T1 | -1.139706 | IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005153-T1 | -1.141212 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009787-T1 | -1.141882 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008527-T1 | -1.142627 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009812-T1 | -1.143459 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006215-T1 | -1.145166 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001925-T1 | -1.145918 | IPR001841 Zinc finger, RING-type, IPR002867 IBR domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006992-T1 | -1.146775 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010010-T1 | -1.146789 | IPR036013 Band 7/SPFH domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009594-T1 | -1.149357 | IPR002877 Ribosomal RNA methyltransferase, FtsJ domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005832-T1 | -1.150654 | IPR009836 Glycine-rich domain-containing protein-like | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006250-T1 | -1.153982 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002478-T1 | -1.154555 | IPR013126 Heat shock protein 70 family, IPR043129 ATPase, nucleotide binding domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003033-T1 | -1.155116 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002477-T1 | -1.157099 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010530-T1 | -1.158664 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001222-T1 | -1.167774 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009738-T1 | -1.170585 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006766-T1 | -1.171555 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010007-T1 | -1.175289 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009438-T1 | -1.175488 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003238-T1 | -1.177022 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009437-T1 | -1.179555 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010368-T1 | -1.180001 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001509-T1 | -1.181146 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001462-T1 | -1.182311 | IPR008775 Phytanoyl-CoA dioxygenase-like | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005177-T1 | -1.185673 | IPR001313 Pumilio RNA-binding repeat, IPR011989 Armadillo-like helical, IPR016024 Armadillo-type fold, IPR033133 Pumilio homology domain, IPR033712 Pumilio, RNA binding domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001839-T1 | -1.189988 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009785-T1 | -1.191020 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007467-T1 | -1.203546 | IPR013830 SGNH hydrolase-type esterase domain, IPR036514 SGNH hydrolase superfamily | CE3 | NA | TRUE | FALSE | |
| XANPAGTX0501_010638-T1 | -1.203845 | IPR003593 AAA+ ATPase domain, IPR003959 ATPase, AAA-type, core, IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008862-T1 | -1.204663 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008420-T1 | -1.205385 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010529-T1 | -1.212807 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001648-T1 | -1.214948 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005677-T1 | -1.220573 | IPR004313 Acireductone dioxygenase ARD family, IPR011051 RmlC-like cupin domain superfamily, IPR014710 RmlC-like jelly roll fold, IPR027496 Acireductone dioxygenase, eukaryotes | NA | NA | K08967 | FALSE | FALSE |
| XANPAGTX0501_005317-T1 | -1.226163 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_005370-T1 | -1.231519 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000888-T1 | -1.234664 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009407-T1 | -1.241242 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009599-T1 | -1.242828 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006143-T1 | -1.243856 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000622-T1 | -1.244489 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007851-T1 | -1.245823 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001498-T1 | -1.248272 | IPR012340 Nucleic acid-binding, OB-fold | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008005-T1 | -1.251448 | IPR001965 Zinc finger, PHD-type, IPR011011 Zinc finger, FYVE/PHD-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR019786 Zinc finger, PHD-type, conserved site, IPR019787 Zinc finger, PHD-finger | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005952-T1 | -1.253184 | IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000707-T1 | -1.255320 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003775-T2 | -1.260916 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K11593 | FALSE | FALSE |
| XANPAGTX0501_005280-T1 | -1.264296 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003264-T1 | -1.264968 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008708-T1 | -1.265455 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001062-T1 | -1.268232 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006095-T1 | -1.272978 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009628-T1 | -1.276921 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004596-T1 | -1.281428 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004753-T1 | -1.281897 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000281-T1 | -1.282182 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003198-T1 | -1.286713 | IPR022085 Oxopyrrolidines biosynthesis cluster protein G | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010276-T1 | -1.289004 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010523-T1 | -1.289004 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007934-T1 | -1.291157 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002054-T1 | -1.291837 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005550-T1 | -1.294683 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005188-T1 | -1.298616 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004102-T1 | -1.299115 | IPR000420 Yeast PIR protein repeat | NA | NA | K26550 | TRUE | FALSE |
| XANPAGTX0501_002019-T1 | -1.299594 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010021-T1 | -1.299618 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002159-T1 | -1.301773 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002946-T1 | -1.307564 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003790-T1 | -1.311097 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002123-T1 | -1.312729 | IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily | NA | NA | K11699 | FALSE | FALSE |
| XANPAGTX0501_000751-T1 | -1.312812 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001644-T1 | -1.313601 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007232-T1 | -1.314325 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006139-T1 | -1.315900 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001436-T1 | -1.320276 | IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006420-T1 | -1.320799 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005281-T1 | -1.324225 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004466-T1 | -1.328900 | IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002098-T1 | -1.334348 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007833-T1 | -1.343993 | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004270-T1 | -1.346903 | IPR009465 Spondin, N-terminal | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003124-T1 | -1.348872 | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain | NA | A01A | TRUE | FALSE | |
| XANPAGTX0501_000938-T1 | -1.358336 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007254-T1 | -1.362647 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010211-T1 | -1.362647 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008200-T1 | -1.362879 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003864-T1 | -1.363940 | IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005775-T1 | -1.364250 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007473-T1 | -1.375934 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007936-T1 | -1.379176 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005640-T1 | -1.380432 | IPR013087 Zinc finger C2H2-type | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000026-T1 | -1.381814 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010180-T1 | -1.383532 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010275-T1 | -1.384204 | IPR003593 AAA+ ATPase domain, IPR027417 P-loop containing nucleoside triphosphate hydrolase, IPR041679 DNA2/NAM7 helicase-like, C-terminal | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006203-T1 | -1.386200 | IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001955-T1 | -1.387192 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009761-T1 | -1.387848 | IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily | NA | NA | K20412 | TRUE | FALSE |
| XANPAGTX0501_002410-T1 | -1.391729 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006114-T1 | -1.393540 | IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily | NA | NA | K12782 | FALSE | FALSE |
| XANPAGTX0501_007365-T1 | -1.397815 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009326-T1 | -1.398307 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005584-T1 | -1.398387 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001825-T1 | -1.402807 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010380-T1 | -1.404538 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000033-T1 | -1.410231 | IPR002656 Acyltransferase 3 domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009293-T1 | -1.419596 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_004008-T1 | -1.420375 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000036-T1 | -1.420457 | IPR006640 SprT-like | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009581-T1 | -1.427218 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008888-T1 | -1.427796 | IPR007527 Zinc finger, SWIM-type | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003765-T1 | -1.428029 | IPR000420 Yeast PIR protein repeat | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_000697-T1 | -1.443805 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_006214-T1 | -1.444244 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009795-T2 | -1.444535 | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010304-T1 | -1.458420 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006422-T1 | -1.460727 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004978-T1 | -1.460984 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009621-T1 | -1.461288 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006909-T1 | -1.464054 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008863-T1 | -1.466559 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002007-T1 | -1.467093 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_002820-T1 | -1.467192 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006246-T1 | -1.468497 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007869-T1 | -1.472330 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005619-T1 | -1.474796 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010379-T1 | -1.475645 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008874-T1 | -1.479109 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006459-T1 | -1.480266 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009605-T1 | -1.480669 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002963-T1 | -1.487093 | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | AA3 | NA | K00108 | TRUE | FALSE |
| XANPAGTX0501_009942-T1 | -1.494661 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001951-T1 | -1.498238 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004853-T1 | -1.500419 | IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003361-T1 | -1.505428 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001820-T2 | -1.510192 | IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000691-T1 | -1.511934 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001710-T1 | -1.512838 | IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases | GT32 | NA | FALSE | FALSE | |
| XANPAGTX0501_003448-T1 | -1.515924 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_000420-T1 | -1.518444 | IPR013087 Zinc finger C2H2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005278-T1 | -1.521181 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010051-T1 | -1.529828 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000910-T1 | -1.530331 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009511-T1 | -1.533303 | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | GH16 | NA | K01216 | TRUE | FALSE |
| XANPAGTX0501_008533-T1 | -1.540302 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009737-T1 | -1.540774 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009141-T1 | -1.543886 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007899-T1 | -1.544599 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003247-T1 | -1.545289 | IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily | NA | NA | K09250 | FALSE | FALSE |
| XANPAGTX0501_009666-T1 | -1.554891 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001082-T1 | -1.559541 | IPR004853 Sugar phosphate transporter domain | NA | NA | K26222 | FALSE | FALSE |
| XANPAGTX0501_005402-T1 | -1.560177 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000872-T1 | -1.562878 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005296-T1 | -1.568716 | IPR018750 Protein of unknown function DUF2306, membrane | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004018-T2 | -1.571979 | IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007750-T1 | -1.577297 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004416-T1 | -1.578773 | IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 | NA | T02 | K08657 | FALSE | FALSE |
| XANPAGTX0501_007403-T1 | -1.582309 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010598-T1 | -1.582325 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009600-T1 | -1.583776 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007231-T1 | -1.583790 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010381-T1 | -1.592206 | IPR002293 Amino acid/polyamine transporter I | NA | NA | K03294 | FALSE | FALSE |
| XANPAGTX0501_008534-T1 | -1.593016 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001512-T1 | -1.603338 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001061-T1 | -1.603339 | IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001953-T1 | -1.607205 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005049-T1 | -1.612235 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002057-T1 | -1.616294 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008008-T1 | -1.617050 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006330-T1 | -1.618394 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001064-T1 | -1.621988 | IPR021765 Mycotoxin biosynthesis protein UstYa-like | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009887-T1 | -1.625740 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001965-T1 | -1.632952 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008628-T1 | -1.639869 | IPR023346 Lysozyme-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000025-T1 | -1.641669 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001362-T1 | -1.647839 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003283-T1 | -1.648782 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001948-T1 | -1.662753 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001888-T1 | -1.678493 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001950-T1 | -1.678963 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007464-T1 | -1.685849 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002213-T1 | -1.688746 | IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009316-T1 | -1.697722 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009886-T1 | -1.705744 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_003282-T1 | -1.706541 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008426-T1 | -1.707030 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001330-T1 | -1.707882 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000681-T1 | -1.709567 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001964-T1 | -1.727590 | IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001949-T1 | -1.732732 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006245-T1 | -1.743213 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_003212-T1 | -1.757104 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009317-T1 | -1.758003 | IPR008979 Galactose-binding-like domain superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009582-T1 | -1.765103 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004217-T1 | -1.766312 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | K24990 | FALSE | FALSE |
| XANPAGTX0501_005394-T1 | -1.767362 | IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001947-T1 | -1.767840 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003775-T1 | -1.770114 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K11593 | FALSE | FALSE |
| XANPAGTX0501_008419-T1 | -1.778819 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004950-T1 | -1.782824 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002170-T1 | -1.786506 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000893-T1 | -1.791529 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004628-T1 | -1.792127 | IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K03469 | FALSE | FALSE |
| XANPAGTX0501_007343-T1 | -1.792140 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004494-T1 | -1.792536 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010117-T1 | -1.793767 | IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | NA | NA | K15523 | FALSE | FALSE |
| XANPAGTX0501_006449-T1 | -1.796457 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000005-T1 | -1.801160 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005658-T1 | -1.801278 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003213-T1 | -1.804291 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001954-T1 | -1.808672 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004580-T1 | -1.809609 | IPR007292 Nuclear fusion protein Kar5 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002103-T1 | -1.810531 | IPR036910 High mobility group box domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005597-T1 | -1.816345 | IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain | GH133 | NA | K01196 | FALSE | FALSE |
| XANPAGTX0501_005613-T1 | -1.817996 | IPR003615 HNH nuclease | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006016-T1 | -1.831989 | IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal | GH63 | NA | FALSE | FALSE | |
| XANPAGTX0501_002104-T1 | -1.835003 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007067-T1 | -1.839308 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001612-T1 | -1.846971 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000398-T1 | -1.847702 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004493-T1 | -1.857771 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007244-T1 | -1.858539 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000610-T1 | -1.868687 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001333-T1 | -1.870374 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009927-T1 | -1.870484 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007870-T1 | -1.874070 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004104-T1 | -1.878122 | IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005631-T1 | -1.885566 | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009786-T1 | -1.894942 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002185-T1 | -1.897085 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002163-T1 | -1.904022 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006255-T1 | -1.904541 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001643-T1 | -1.910689 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010222-T1 | -1.912114 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002166-T1 | -1.917720 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009926-T1 | -1.919959 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000194-T1 | -1.934433 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | K01176 | FALSE | FALSE |
| XANPAGTX0501_000647-T1 | -1.940161 | IPR000571 Zinc finger, CCCH-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001956-T1 | -1.941094 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008090-T1 | -1.954350 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002165-T1 | -1.959472 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005620-T1 | -1.973360 | IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004520-T1 | -1.985803 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001605-T1 | -1.990522 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001538-T1 | -1.994056 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001414-T1 | -1.994528 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005048-T1 | -1.997677 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000604-T1 | -1.997943 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001958-T1 | -1.998637 | IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006974-T1 | -2.000740 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009615-T1 | -2.000853 | IPR035940 CAP superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001952-T1 | -2.002699 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008041-T1 | -2.016189 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_005630-T1 | -2.027229 | IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002522-T1 | -2.030035 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006910-T1 | -2.032529 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001967-T1 | -2.032808 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003572-T1 | -2.044217 | IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily | CE16 | NA | TRUE | FALSE | |
| XANPAGTX0501_010303-T1 | -2.054768 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005279-T1 | -2.055973 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009139-T1 | -2.056685 | IPR001876 Zinc finger, RanBP2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004891-T1 | -2.057500 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001910-T1 | -2.062241 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007873-T1 | -2.067522 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007871-T1 | -2.081123 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005615-T1 | -2.092197 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009318-T1 | -2.097684 | IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005735-T1 | -2.102015 | IPR018824 Conidiation-specific protein 6 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007872-T1 | -2.105800 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001611-T1 | -2.125697 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005814-T1 | -2.129685 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001859-T1 | -2.142380 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007262-T1 | -2.149005 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010203-T1 | -2.149005 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008856-T1 | -2.160218 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005061-T1 | -2.166875 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002183-T1 | -2.174606 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002182-T1 | -2.180402 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002763-T1 | -2.184556 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009619-T1 | -2.203533 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005766-T1 | -2.223453 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004414-T1 | -2.230880 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006957-T1 | -2.252415 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005614-T1 | -2.252890 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001960-T1 | -2.264721 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010596-T1 | -2.271872 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000193-T1 | -2.283992 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | FALSE | FALSE | |
| XANPAGTX0501_004521-T1 | -2.284391 | IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002172-T1 | -2.285092 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008331-T1 | -2.302060 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002184-T1 | -2.304675 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004966-T1 | -2.317059 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001959-T1 | -2.362237 | IPR000095 CRIB domain, IPR000719 Protein kinase domain, IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily, IPR017441 Protein kinase, ATP binding site, IPR033923 p21 activated kinase binding domain, IPR036936 CRIB domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001063-T1 | -2.369606 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_008284-T1 | -2.429045 | IPR029044 Nucleotide-diphospho-sugar transferases | GT2_Glyco_tranf_2 | NA | FALSE | FALSE | |
| XANPAGTX0501_008782-T1 | -2.431407 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001966-T1 | -2.436706 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003209-T1 | -2.437600 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008009-T1 | -2.444813 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001962-T1 | -2.456164 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008007-T1 | -2.479715 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007397-T1 | -2.486783 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000378-T1 | -2.490902 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009602-T1 | -2.500879 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006951-T1 | -2.507920 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002164-T1 | -2.527734 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001856-T1 | -2.592477 | IPR037176 Osmotin/thaumatin-like superfamily | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_007900-T1 | -2.636563 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006327-T1 | -2.649849 | IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002506-T1 | -2.726475 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010050-T2 | -2.757580 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003211-T1 | -2.931999 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007239-T1 | -3.420906 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008519-T2 | -4.617470 | NA | NA | NA | FALSE | FALSE |
mult_gene_table_ap2<-mult_gene_table %>% inner_join(ea_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap2 %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | ID | Annotation_type | Description | Function | Function_type | b |
|---|---|---|---|---|---|---|
| XANPAGTX0501_001061-T1 | IPR013149 | IPR | Alcohol dehydrogenase-like, C-terminal | Acetyl-CoA production and metabolism | Fungal multicellularity | -1.603339 |
| XANPAGTX0501_005597-T1 | IPR032788 | IPR | Glycogen debranching enzyme, central domain | Carbohydrate storage | Fungal multicellularity | -1.816345 |
| XANPAGTX0501_000647-T1 | IPR000571 | IPR | Zinc finger, CCCH-type | Cell division, proliferation and growth | Fungal multicellularity | -1.940161 |
| XANPAGTX0501_002213-T1 | IPR001650 | IPR | Helicase, C-terminal | Cell division, proliferation and growth | Fungal multicellularity | -1.688746 |
| XANPAGTX0501_003775-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.770114 |
| XANPAGTX0501_003775-T2 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.260916 |
| XANPAGTX0501_004104-T1 | IPR001214 | IPR | SET domain | Cell division, proliferation and growth | Fungal multicellularity | -1.878122 |
| XANPAGTX0501_004244-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.139706 |
| XANPAGTX0501_004628-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.792127 |
| XANPAGTX0501_003124-T1 | IPR001461 | IPR | Aspartic peptidase A1 family | Cell surface and cell wall proteins | Fungal multicellularity | -1.348872 |
| XANPAGTX0501_005735-T1 | IPR018824 | IPR | Conidiation-specific protein 6 | Cell surface and cell wall proteins | Fungal multicellularity | -2.102015 |
| XANPAGTX0501_006327-T1 | IPR018466 | IPR | Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | Cell wall biosynthesis | Fungal multicellularity | -2.649849 |
| XANPAGTX0501_000203-T1 | IPR037176 | IPR | Osmotin/thaumatin-like superfamily | Cell wall remodeling | Fungal multicellularity | -1.040557 |
| XANPAGTX0501_001856-T1 | IPR037176 | IPR | Osmotin/thaumatin-like superfamily | Cell wall remodeling | Fungal multicellularity | -2.592477 |
| XANPAGTX0501_007833-T1 | IPR002889 | IPR | Carbohydrate-binding WSC | Cell wall remodeling | Fungal multicellularity | -1.343993 |
| XANPAGTX0501_009511-T1 | GH16 | CAZy | act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans | Cell wall remodeling | Fungal multicellularity | -1.533303 |
| XANPAGTX0501_006767-T1 | IPR017956 | IPR | AT hook, DNA-binding motif | Chromatin regulation | Expression regulation | -1.001121 |
| XANPAGTX0501_001064-T1 | IPR021765 | IPR | Mycotoxin biosynthesis protein UstYa-like | Defense | Fungal multicellularity | -1.621988 |
| XANPAGTX0501_001643-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.910689 |
| XANPAGTX0501_003212-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.757104 |
| XANPAGTX0501_003213-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.804291 |
| XANPAGTX0501_003264-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.264968 |
| XANPAGTX0501_005550-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.294683 |
| XANPAGTX0501_005620-T1 | IPR017907 | IPR | Zinc finger; RING-type; conserved site | Protein ubiquitination | Fungal multicellularity | -1.973360 |
| XANPAGTX0501_006203-T1 | IPR017907 | IPR | Zinc finger; RING-type; conserved site | Protein ubiquitination | Fungal multicellularity | -1.386200 |
| XANPAGTX0501_007869-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.472330 |
| XANPAGTX0501_008856-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -2.160218 |
| XANPAGTX0501_009316-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.697722 |
| XANPAGTX0501_009738-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.170585 |
| XANPAGTX0501_009942-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.494661 |
| XANPAGTX0501_010380-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.404538 |
| XANPAGTX0501_001648-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.214948 |
| XANPAGTX0501_002098-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.334348 |
| XANPAGTX0501_002123-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.312729 |
| XANPAGTX0501_004217-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.766312 |
| XANPAGTX0501_005177-T1 | IPR001313 | IPR | Pumilio RNA-binding repeat | RNA binding proteins | Expression regulation | -1.185673 |
| XANPAGTX0501_002123-T1 | IPR007855 | IPR | RNA-dependent RNA polymerase, eukaryotic-type | RNA interference | Expression regulation | -1.312729 |
| XANPAGTX0501_003775-T1 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.770114 |
| XANPAGTX0501_003775-T2 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.260916 |
| XANPAGTX0501_004244-T1 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.139706 |
| XANPAGTX0501_000420-T1 | IPR013087 | IPR | Zinc finger C2H2-type | Transcription factors | Expression regulation | -1.518444 |
| XANPAGTX0501_001955-T1 | IPR036864 | IPR | Zn(2)-C6 fungal-type DNA-binding domain superfamily | Transcription factors | Expression regulation | -1.387192 |
| XANPAGTX0501_001958-T1 | IPR001356 | IPR | Homeobox domain | Transcription factors | Expression regulation | -1.998637 |
| XANPAGTX0501_005620-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.973360 |
| XANPAGTX0501_005640-T1 | IPR013087 | IPR | Zinc finger C2H2-type | Transcription factors | Expression regulation | -1.380432 |
| XANPAGTX0501_006203-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.386200 |
| XANPAGTX0501_006931-T1 | IPR013087 | IPR | Zinc finger C2H2-type | Transcription factors | Expression regulation | -1.072494 |
| XANPAGTX0501_008005-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.251448 |
| XANPAGTX0501_000281-T1 | IPR036259 | IPR | MFS transporter superfamily | Transporters | Fungal multicellularity | -1.282182 |
| XANPAGTX0501_001825-T1 | IPR036259 | IPR | MFS transporter superfamily | Transporters | Fungal multicellularity | -1.402807 |
| XANPAGTX0501_008594-T1 | IPR036259 | IPR | MFS transporter superfamily | Transporters | Fungal multicellularity | -1.040188 |
| XANPAGTX0501_009737-T1 | IPR036259 | IPR | MFS transporter superfamily | Transporters | Fungal multicellularity | -1.540774 |
Notably, many TFs and ubiquitin degradation proteins
Also many transporters, which wasn’t the case in other lists here
Enrichment analysis
enrich2<-clusterProfiler::enricher(ap_ea_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise2<-enrichplot::pairwise_termsim(enrich2)
enrichplot::emapplot(enrich_pairwise2)
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.max(ea_sig$b)],
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = ea_sig$target_id[which.max(ea_sig$b[-which.max(ea_sig$b)])],
units = "est_counts",
color_by = "part")
ed_ea_genes<-ea_sig %>% filter(change=="edge") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ed_ea_genes %>%
kable(format = "html", col.names = colnames(ap_ea_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_010431-T1 | 1.523359 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001015-T1 | 1.339807 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_006189-T1 | 1.275509 | IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002706-T1 | 1.129817 | IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004034-T1 | 1.121819 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_010624-T1 | 1.121535 | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_004943-T2 | 1.117316 | IPR002020 Citrate synthase, IPR016142 Citrate synthase-like, large alpha subdomain, IPR016143 Citrate synthase-like, small alpha subdomain, IPR019810 Citrate synthase active site, IPR036969 Citrate synthase superfamily | NA | NA | K01647 | FALSE | FALSE |
| XANPAGTX0501_006869-T1 | 1.099929 | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | GH128 | NA | TRUE | FALSE | |
| XANPAGTX0501_004633-T1 | 1.094695 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010430-T1 | 1.093667 | IPR000542 Acyltransferase ChoActase/COT/CPT, IPR001227 Acyl transferase domain superfamily, IPR006162 Phosphopantetheine attachment site, IPR009081 Phosphopantetheine binding ACP domain, IPR011032 GroES-like superfamily, IPR013217 Methyltransferase type 12, IPR013968 Polyketide synthase, ketoreductase domain, IPR014030 Beta-ketoacyl synthase, N-terminal, IPR014031 Beta-ketoacyl synthase, C-terminal, IPR014043 Acyl transferase, IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase, IPR016036 Malonyl-CoA ACP transacylase, ACP-binding, IPR016039 Thiolase-like, IPR020801 None, IPR020806 Polyketide synthase, phosphopantetheine-binding domain, IPR020807 Polyketide synthase, dehydratase domain, IPR020841 Polyketide synthase, beta-ketoacyl synthase domain, IPR020843 Polyketide synthase, enoylreductase domain, IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily, IPR032821 Polyketide synthase, C-terminal extension, IPR036291 NAD(P)-binding domain superfamily, IPR036736 ACP-like superfamily, IPR039551 Choline/carnitine acyltransferase domain, IPR042104 Polyketide synthase, dehydratase domain superfamily, IPR042231 Choline/Carnitine o-acyltransferase, domain 2, IPR042232 None | NA | NA | K12443 | FALSE | TRUE |
| XANPAGTX0501_001458-T1 | 1.026449 | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009181-T1 | 1.024662 | IPR008427 Extracellular membrane protein, CFEM domain | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_008853-T1 | 1.003145 | IPR009799 EthD domain, IPR011008 Dimeric alpha-beta barrel | NA | NA | FALSE | FALSE |
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_008853-T1",
units = "est_counts",
color_by = "part")
plot_bootstrap(ea_so,
target_id = "XANPAGTX0501_008852-T1",
units = "est_counts",
color_by = "part")
ggplot(ea_table)+geom_histogram(aes(x=qval))
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 690798 rows containing non-finite values (`stat_bin()`).
library(MKpower)
qqunif(ea_table$qval, color.line = "orange")
library(ggVennDiagram)
##
## Attaching package: 'ggVennDiagram'
## The following object is masked from 'package:tidyr':
##
## unite
venn_e<-list(compared_to_apothecia = ea_sig$target_id[ea_sig$change=="edge"],
compared_to_center = ec_sig$target_id[ec_sig$b>0.9])
e<-ggVennDiagram(venn_e,label_size = 5,set_size=5)+labs(title = "Upregulated in edge")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
e
venn_c<-list(compared_to_apothecia = ca_sig$target_id[ca_sig$change=="centre"],
compared_to_edge = ec_sig$target_id[ec_sig$change=="centre"])
c<-ggVennDiagram(venn_c,label_size = 5,set_size=5)+labs(title = "Upregulated in center")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
c
venn_a<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"])
a<-ggVennDiagram(venn_a,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a
Since there was so little difference between edge and center, pooled them together
250 upregulated in apothecia, only 2 in thallus
kal_dirs2 <-kal_dirs2 %>% mutate(part2 = ifelse(part =="apothecia","apothecia","thallus") )
kal_dirs2$part2 <- as.factor(kal_dirs2$part2)
kal_dirs2$thallus<- as.factor(kal_dirs2$thallus)
rhdf5::h5closeAll()
a_so <- sleuth_prep(kal_dirs2,extra_bootstrap_summary = TRUE,filter_target_id = target_id,transformation_function = function(x) log2(x + 0.1))
## Warning in check_num_cores(num_cores): It appears that you are running Sleuth from within Rstudio.
## Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
## If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
## reading in kallisto results
## dropping unused factor levels
## .................
## normalizing est_counts
## A list of target IDs for filtering was found. Using this for filtering
## 11083 targets passed the filter
## normalizing tpm
## merging in metadata
## summarizing bootstraps
## .................
#model that includes only confounding variables
a_so <- sleuth_fit(a_so, ~thallus, 'reduced')
## fitting measurement error models
## shrinkage estimation
## 1 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1
## computing variance of betas
#model that includes only both the confounding variable and the variable of interest
a_so <- sleuth_fit(a_so, ~ thallus + part2, 'full')
## fitting measurement error models
## shrinkage estimation
## 4 NA values were found during variance shrinkage estimation due to mean observation values outside of the range used for the LOESS fit.
## The LOESS fit will be repeated using exact computation of the fitted surface to extrapolate the missing values.
## These are the target ids with NA values: XANPAGTX0501_000967-T1, XANPAGTX0501_001127-T1, XANPAGTX0501_002409-T1, XANPAGTX0501_010086-T1
## computing variance of betas
#compare the models
a_so <- sleuth_lrt(a_so, 'reduced', 'full')
a_so <- sleuth_wt(a_so, 'part2thallus')
a_table <- sleuth_results(a_so, 'part2thallus')
a_sig <- a_table %>% tibble::as_tibble() %>%
filter( qval <= 0.05, grepl("GTX0501",target_id) ) %>%
arrange(desc(b)) %>% mutate(change = if_else(b > 1, "thallus", ifelse(b< -1, "apothecium", "low_logFC")))
table(a_sig$change)
##
## apothecium low_logFC thallus
## 250 2746 2
library(RColorBrewer)
color_scheme<-c("apothecia"=brewer.pal(3,"Dark2")[1],
"thallus_centre"=brewer.pal(3,"Dark2")[2],
"thallus_edge" =brewer.pal(3,"Dark2")[3] )
plot_pca(a_so, color_by = 'part', text_labels = TRUE,use_filtered=T)+
theme_bw()+theme(text=element_text(size=7))+
scale_color_manual(values=color_scheme)
ggsave('../results/tissue_pca.pdf',width = 4.5, height = 3)
plot_bootstrap(a_so,
target_id = a_sig$target_id[which.max(a_sig$b)],
units = "est_counts",
color_by = "part2")
plot_bootstrap(a_so,
target_id = a_sig$target_id[which.max(a_sig$b[-which.max(a_sig$b)])],
units = "est_counts",
color_by = "part2")
a_genes<-a_sig %>% filter(b>0.9) %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
a_genes %>%
kable(format = "html", col.names = colnames(a_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_009376-T1 | 2.4961545 | IPR043141 Ribosomal protein L10-like domain superfamily | NA | NA | K02864 | FALSE | FALSE |
| XANPAGTX0501_004633-T1 | 1.0318823 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009913-T1 | 0.9922726 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002706-T1 | 0.9523073 | IPR002129 Pyridoxal phosphate-dependent decarboxylase, IPR015421 Pyridoxal phosphate-dependent transferase, major domain, IPR015424 Pyridoxal phosphate-dependent transferase | NA | NA | FALSE | FALSE |
ap_a_genes<-a_sig %>% filter(change=="apothecium") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho)
ap_a_genes %>%
kable(format = "html", col.names = colnames(ap_a_genes)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho |
|---|---|---|---|---|---|---|---|
| XANPAGTX0501_007851-T1 | -1.000996 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009787-T1 | -1.001679 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000938-T1 | -1.002687 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007833-T1 | -1.003237 | IPR002889 Carbohydrate-binding WSC, IPR018535 Domain of unknown function DUF1996 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001498-T1 | -1.006175 | IPR012340 Nucleic acid-binding, OB-fold | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005188-T1 | -1.006230 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003775-T2 | -1.015597 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K11593 | FALSE | FALSE |
| XANPAGTX0501_007473-T1 | -1.021407 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003790-T1 | -1.024429 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006420-T1 | -1.025603 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001955-T1 | -1.028447 | IPR001138 Zn(2)Cys(6) fungal-type DNA-binding domain, IPR001451 Hexapeptide repeat, IPR002110 Ankyrin repeat, IPR011004 Trimeric LpxA-like superfamily, IPR018357 Hexapeptide transferase, conserved site, IPR020683 Domain of unknown function DUF3447, IPR024688 Maltose/galactoside acetyltransferase, IPR036770 Ankyrin repeat-containing domain superfamily, IPR036864 Zn(2)-C6 fungal-type DNA-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003033-T1 | -1.030286 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002054-T1 | -1.034049 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_003124-T1 | -1.035285 | IPR001461 Aspartic peptidase A1 family, IPR001969 Aspartic peptidase, active site, IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain, IPR034164 Pepsin-like domain | NA | A01A | TRUE | FALSE | |
| XANPAGTX0501_002946-T1 | -1.035401 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002142-T1 | -1.036917 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009581-T1 | -1.037279 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004753-T1 | -1.037567 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003765-T1 | -1.038156 | IPR000420 Yeast PIR protein repeat | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_004978-T1 | -1.047426 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_004466-T1 | -1.048483 | IPR000490 Glycoside hydrolase family 17, IPR017853 Glycoside hydrolase superfamily, IPR018620 Ubiquitin 3 binding protein But2, C-terminal | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_006422-T1 | -1.053965 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005317-T1 | -1.054307 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_006975-T1 | -1.054818 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000622-T1 | -1.055181 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002098-T1 | -1.056175 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007365-T1 | -1.056362 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004102-T1 | -1.058681 | IPR000420 Yeast PIR protein repeat | NA | NA | K26550 | TRUE | FALSE |
| XANPAGTX0501_001825-T1 | -1.063406 | IPR003663 Sugar/inositol transporter, IPR005828 Major facilitator, sugar transporter-like, IPR005829 Sugar transporter, conserved site, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001223-T1 | -1.064214 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005815-T1 | -1.064277 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000036-T1 | -1.068838 | IPR006640 SprT-like | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002019-T1 | -1.070414 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005619-T1 | -1.070482 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009599-T1 | -1.070929 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001964-T1 | -1.071179 | IPR001611 Leucine-rich repeat, IPR003591 Leucine-rich repeat, typical subtype, IPR019487 RAM signalling pathway, SOG2, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000888-T1 | -1.071659 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009795-T2 | -1.071736 | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008200-T1 | -1.073076 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008888-T1 | -1.075701 | IPR007527 Zinc finger, SWIM-type | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010001-T1 | -1.075953 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010379-T1 | -1.076421 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001965-T1 | -1.078800 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010094-T1 | -1.079269 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006459-T1 | -1.089552 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002123-T1 | -1.092697 | IPR000504 RNA recognition motif domain, IPR007855 RNA-dependent RNA polymerase, eukaryotic-type, IPR035979 RNA-binding domain superfamily | NA | NA | K11699 | FALSE | FALSE |
| XANPAGTX0501_009326-T1 | -1.097552 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001948-T1 | -1.099351 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009293-T1 | -1.101651 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007899-T1 | -1.103335 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000420-T1 | -1.104047 | IPR013087 Zinc finger C2H2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006246-T1 | -1.104366 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006114-T1 | -1.104804 | IPR001680 WD40 repeat, IPR015943 WD40/YVTN repeat-like-containing domain superfamily, IPR036322 WD40-repeat-containing domain superfamily | NA | NA | K12782 | FALSE | FALSE |
| XANPAGTX0501_006310-T1 | -1.105045 | IPR022137 Zinc finger protein, DUF3669 domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001963-T1 | -1.111833 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004008-T1 | -1.117183 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002410-T1 | -1.117363 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002963-T1 | -1.118354 | IPR000172 Glucose-methanol-choline oxidoreductase, N-terminal, IPR007867 Glucose-methanol-choline oxidoreductase, C-terminal, IPR012132 Glucose-methanol-choline oxidoreductase, IPR036188 FAD/NAD(P)-binding domain superfamily | AA3 | NA | K00108 | TRUE | FALSE |
| XANPAGTX0501_006909-T1 | -1.120330 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010145-T1 | -1.120565 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005584-T1 | -1.124341 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002007-T1 | -1.126910 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_005278-T1 | -1.128439 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000872-T1 | -1.128589 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001710-T1 | -1.130646 | IPR007577 Glycosyltransferase, DXD sugar-binding motif, IPR029044 Nucleotide-diphospho-sugar transferases | GT32 | NA | FALSE | FALSE | |
| XANPAGTX0501_007869-T1 | -1.136332 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009511-T1 | -1.136478 | IPR000757 Glycoside hydrolase family 16, IPR001002 Chitin-binding, type 1, IPR008264 Beta-glucanase, IPR013320 Concanavalin A-like lectin/glucanase domain superfamily, IPR036861 Endochitinase-like superfamily | GH16 | NA | K01216 | TRUE | FALSE |
| XANPAGTX0501_000691-T1 | -1.140810 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010007-T1 | -1.146366 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001820-T2 | -1.147375 | IPR021109 Aspartic peptidase domain superfamily, IPR033121 Peptidase family A1 domain | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008863-T1 | -1.149308 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010381-T1 | -1.157248 | IPR002293 Amino acid/polyamine transporter I | NA | NA | K03294 | FALSE | FALSE |
| XANPAGTX0501_003361-T1 | -1.157393 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_009666-T1 | -1.163354 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000910-T1 | -1.164861 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009942-T1 | -1.164912 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008874-T1 | -1.168644 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005296-T1 | -1.170842 | IPR018750 Protein of unknown function DUF2306, membrane | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004853-T1 | -1.170891 | IPR000719 Protein kinase domain, IPR000961 AGC-kinase, C-terminal, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001512-T1 | -1.171326 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006203-T1 | -1.175049 | IPR001841 Zinc finger, RING-type, IPR002867 IBR domain, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001436-T1 | -1.178216 | IPR002048 EF-hand domain, IPR011992 EF-hand domain pair, IPR018247 EF-Hand 1, calcium-binding site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007750-T1 | -1.181450 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002820-T1 | -1.183558 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010051-T1 | -1.184568 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003247-T1 | -1.184643 | IPR001878 Zinc finger, CCHC-type, IPR025836 Zinc knuckle CX2CX4HX4C, IPR036875 Zinc finger, CCHC-type superfamily | NA | NA | K09250 | FALSE | FALSE |
| XANPAGTX0501_009621-T1 | -1.188204 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005620-T1 | -1.188513 | IPR001841 Zinc finger, RING-type, IPR004331 SPX domain, IPR011016 Zinc finger, RING-CH-type, IPR013083 Zinc finger, RING/FYVE/PHD-type, IPR017907 Zinc finger, RING-type, conserved site | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009321-T1 | -1.190228 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003448-T1 | -1.191987 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_009141-T1 | -1.192722 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009887-T1 | -1.200786 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_000610-T1 | -1.207426 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001643-T1 | -1.215746 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010380-T1 | -1.223224 | IPR000210 BTB/POZ domain, IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007403-T1 | -1.228285 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001082-T1 | -1.232060 | IPR004853 Sugar phosphate transporter domain | NA | NA | K26222 | FALSE | FALSE |
| XANPAGTX0501_004416-T1 | -1.234261 | IPR000246 Peptidase T2, asparaginase 2, IPR029055 Nucleophile aminohydrolases, N-terminal, IPR037464 Threonine aspartase 1 | NA | T02 | K08657 | FALSE | FALSE |
| XANPAGTX0501_001064-T1 | -1.234644 | IPR021765 Mycotoxin biosynthesis protein UstYa-like | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001061-T1 | -1.235309 | IPR002328 Alcohol dehydrogenase, zinc-type, conserved site, IPR011032 GroES-like superfamily, IPR013149 Alcohol dehydrogenase-like, C-terminal, IPR013154 Alcohol dehydrogenase-like, N-terminal, IPR020843 Polyketide synthase, enoylreductase domain, IPR036291 NAD(P)-binding domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004018-T2 | -1.235695 | IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007231-T1 | -1.240318 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009316-T1 | -1.246011 | IPR001810 F-box domain, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003283-T1 | -1.246856 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007244-T1 | -1.249898 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008533-T1 | -1.253515 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007343-T1 | -1.255419 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001952-T1 | -1.257146 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001950-T1 | -1.259001 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002213-T1 | -1.262177 | IPR000629 ATP-dependent RNA helicase DEAD-box, conserved site, IPR001650 Helicase, C-terminal, IPR011545 DEAD/DEAH box helicase domain, IPR014001 Helicase superfamily 1/2, ATP-binding domain, IPR014014 RNA helicase, DEAD-box type, Q motif, IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001951-T1 | -1.262779 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000604-T1 | -1.264223 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010117-T1 | -1.267941 | IPR002110 Ankyrin repeat, IPR011009 Protein kinase-like domain superfamily, IPR016477 Fructosamine/Ketosamine-3-kinase, IPR020683 Domain of unknown function DUF3447, IPR036770 Ankyrin repeat-containing domain superfamily | NA | NA | K15523 | FALSE | FALSE |
| XANPAGTX0501_000697-T1 | -1.273117 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_008628-T1 | -1.274944 | IPR023346 Lysozyme-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001956-T1 | -1.276631 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000398-T1 | -1.277824 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002057-T1 | -1.282644 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001888-T1 | -1.289043 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006449-T1 | -1.291222 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008008-T1 | -1.291576 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003282-T1 | -1.293552 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008426-T1 | -1.294283 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005613-T1 | -1.294861 | IPR003615 HNH nuclease | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007464-T1 | -1.298109 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007870-T1 | -1.300798 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006245-T1 | -1.301264 | NA | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_008420-T1 | -1.301707 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001947-T1 | -1.303157 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006330-T1 | -1.307915 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000892-T1 | -1.309666 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010304-T1 | -1.314210 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001362-T1 | -1.314577 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004628-T1 | -1.317480 | IPR002156 Ribonuclease H domain, IPR012337 Ribonuclease H-like superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K03469 | FALSE | FALSE |
| XANPAGTX0501_001330-T1 | -1.320530 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005658-T1 | -1.322458 | IPR001153 Barwin domain, IPR009009 RlpA-like protein, double-psi beta-barrel domain, IPR036908 RlpA-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005402-T1 | -1.324043 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002165-T1 | -1.325802 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008534-T1 | -1.327391 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002170-T1 | -1.328820 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009317-T1 | -1.330469 | IPR008979 Galactose-binding-like domain superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_005394-T1 | -1.334492 | IPR002575 Aminoglycoside phosphotransferase, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005631-T1 | -1.336475 | IPR023631 Amidase signature domain, IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002103-T1 | -1.336659 | IPR036910 High mobility group box domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008856-T1 | -1.339511 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000681-T1 | -1.344215 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002185-T1 | -1.352061 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003775-T1 | -1.352148 | IPR003100 PAZ domain, IPR003165 Piwi domain, IPR012337 Ribonuclease H-like superfamily, IPR014811 Argonaute, linker 1 domain, IPR032472 Argonaute linker 2 domain, IPR032473 Protein argonaute, Mid domain, IPR032474 Protein argonaute, N-terminal, IPR036085 PAZ domain superfamily, IPR036397 Ribonuclease H superfamily | NA | NA | K11593 | FALSE | FALSE |
| XANPAGTX0501_004580-T1 | -1.355977 | IPR007292 Nuclear fusion protein Kar5 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001010-T1 | -1.356734 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002104-T1 | -1.360844 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004494-T1 | -1.362189 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001859-T1 | -1.367755 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000025-T1 | -1.368135 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_005597-T1 | -1.371604 | IPR006421 Glycogen debranching enzyme, metazoa, IPR008928 Six-hairpin glycosidase superfamily, IPR012341 Six-hairpin glycosidase-like superfamily, IPR017853 Glycoside hydrolase superfamily, IPR029436 Eukaryotic glycogen debranching enzyme, N-terminal domain, IPR032788 Glycogen debranching enzyme, central domain, IPR032790 Glycogen debranching enzyme, C-terminal, IPR032792 Glycogen debranching enzyme, glucanotransferase domain | GH133 | NA | K01196 | FALSE | FALSE |
| XANPAGTX0501_004950-T1 | -1.372326 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005048-T1 | -1.374486 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004217-T1 | -1.376777 | IPR000504 RNA recognition motif domain, IPR012677 Nucleotide-binding alpha-beta plait domain superfamily, IPR035979 RNA-binding domain superfamily | NA | NA | K24990 | FALSE | FALSE |
| XANPAGTX0501_000005-T1 | -1.378844 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003212-T1 | -1.384927 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_002763-T1 | -1.389644 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002163-T1 | -1.392989 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003213-T1 | -1.399730 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004493-T1 | -1.400770 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002166-T1 | -1.400943 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010280-T1 | -1.404057 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006016-T1 | -1.404604 | IPR008928 Six-hairpin glycosidase superfamily, IPR031335 Glycosyl hydrolase family 63, C-terminal | GH63 | NA | FALSE | FALSE | |
| XANPAGTX0501_001333-T1 | -1.411305 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_004104-T1 | -1.419256 | IPR001214 SET domain, IPR011990 Tetratricopeptide-like helical domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007067-T1 | -1.420720 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_007300-T1 | -1.423032 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004414-T1 | -1.423458 | IPR027417 P-loop containing nucleoside triphosphate hydrolase | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001605-T1 | -1.425833 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006255-T1 | -1.434751 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000647-T1 | -1.440550 | IPR000571 Zinc finger, CCCH-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005615-T1 | -1.440903 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006974-T1 | -1.441975 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006957-T1 | -1.443602 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006910-T1 | -1.458293 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001612-T1 | -1.458506 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007871-T1 | -1.463016 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_009582-T1 | -1.469666 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009615-T1 | -1.478640 | IPR035940 CAP superfamily | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_001953-T1 | -1.483265 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009139-T1 | -1.494375 | IPR001876 Zinc finger, RanBP2-type | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005630-T1 | -1.497428 | IPR036928 Amidase signature (AS) superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004891-T1 | -1.501545 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002522-T1 | -1.504550 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005612-T1 | -1.506602 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000893-T1 | -1.508341 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005061-T1 | -1.508665 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007873-T1 | -1.510868 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_001958-T1 | -1.511188 | IPR001356 Homeobox domain, IPR009057 Homeobox-like domain superfamily, IPR017970 Homeobox, conserved site | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000194-T1 | -1.511338 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR013780 Glycosyl hydrolase, all-beta, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | K01176 | FALSE | FALSE |
| XANPAGTX0501_003572-T1 | -1.519271 | IPR001087 GDSL lipase/esterase, IPR036514 SGNH hydrolase superfamily | CE16 | NA | TRUE | FALSE | |
| XANPAGTX0501_002183-T1 | -1.522262 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005279-T1 | -1.523896 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008041-T1 | -1.527220 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_005614-T1 | -1.527719 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001538-T1 | -1.528884 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001954-T1 | -1.534783 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001414-T1 | -1.537299 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001910-T1 | -1.539771 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010303-T1 | -1.542026 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004520-T1 | -1.559567 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007262-T1 | -1.569541 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_010203-T1 | -1.569541 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_008090-T1 | -1.570035 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009318-T1 | -1.577677 | IPR011333 SKP1/BTB/POZ domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002164-T1 | -1.582652 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002184-T1 | -1.584723 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005735-T1 | -1.620055 | IPR018824 Conidiation-specific protein 6 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004521-T1 | -1.625040 | IPR008271 Serine/threonine-protein kinase, active site, IPR011009 Protein kinase-like domain superfamily | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002172-T1 | -1.626040 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001967-T1 | -1.629031 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008009-T1 | -1.631945 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009605-T1 | -1.639551 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009619-T1 | -1.640066 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001611-T1 | -1.646921 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005766-T1 | -1.650350 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_002182-T1 | -1.670548 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008782-T1 | -1.681484 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009786-T1 | -1.691780 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001962-T1 | -1.692967 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007872-T1 | -1.694556 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_006253-T1 | -1.695976 | IPR014849 EKC/KEOPS complex, subunit Gon7 | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008331-T1 | -1.707064 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003209-T1 | -1.709229 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_000193-T1 | -1.729825 | IPR006047 Glycosyl hydrolase, family 13, catalytic domain, IPR017853 Glycoside hydrolase superfamily | GH13 | NA | FALSE | FALSE | |
| XANPAGTX0501_001960-T1 | -1.733269 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_006951-T1 | -1.742660 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008007-T1 | -1.745209 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_010596-T1 | -1.748698 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_005814-T1 | -1.760286 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008284-T1 | -1.771059 | IPR029044 Nucleotide-diphospho-sugar transferases | GT2_Glyco_tranf_2 | NA | FALSE | FALSE | |
| XANPAGTX0501_009926-T1 | -1.775143 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_009602-T1 | -1.777131 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001063-T1 | -1.783787 | NA | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_007397-T1 | -1.849425 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_007900-T1 | -1.867603 | NA | NA | NA | FALSE | TRUE | |
| XANPAGTX0501_000378-T1 | -1.880561 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_004966-T1 | -1.889077 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001856-T1 | -1.894636 | IPR037176 Osmotin/thaumatin-like superfamily | NA | NA | TRUE | TRUE | |
| XANPAGTX0501_006327-T1 | -1.922253 | IPR018466 Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | NA | NA | TRUE | FALSE | |
| XANPAGTX0501_002506-T1 | -1.931043 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_003211-T1 | -2.074356 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_008109-T1 | -2.159140 | IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain | NA | NA | K03800 | FALSE | FALSE |
| XANPAGTX0501_004085-T1 | -2.298435 | IPR000420 Yeast PIR protein repeat | NA | NA | K26550 | TRUE | FALSE |
| XANPAGTX0501_008519-T2 | -2.955922 | NA | NA | NA | FALSE | FALSE | |
| XANPAGTX0501_001156-T3 | -3.105399 | IPR003822 Paired amphipathic helix, IPR013194 Histone deacetylase interacting domain, IPR031693 Sin3, C-terminal, IPR036600 Paired amphipathic helix superfamily | NA | NA | K11644 | FALSE | FALSE |
mult_gene_table_ap3<-mult_gene_table %>% inner_join(a_sig %>% filter(change=="apothecium") %>% select(target_id,b),by=c("TranscriptID"="target_id")) %>% arrange(Function)
mult_gene_table_ap3 %>%
kable(format = "html", col.names = colnames(mult_gene_table_ap3)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "600px")
| TranscriptID | ID | Annotation_type | Description | Function | Function_type | b |
|---|---|---|---|---|---|---|
| XANPAGTX0501_001061-T1 | IPR013149 | IPR | Alcohol dehydrogenase-like, C-terminal | Acetyl-CoA production and metabolism | Fungal multicellularity | -1.235309 |
| XANPAGTX0501_005597-T1 | IPR032788 | IPR | Glycogen debranching enzyme, central domain | Carbohydrate storage | Fungal multicellularity | -1.371604 |
| XANPAGTX0501_000647-T1 | IPR000571 | IPR | Zinc finger, CCCH-type | Cell division, proliferation and growth | Fungal multicellularity | -1.440550 |
| XANPAGTX0501_002213-T1 | IPR001650 | IPR | Helicase, C-terminal | Cell division, proliferation and growth | Fungal multicellularity | -1.262177 |
| XANPAGTX0501_003775-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.352148 |
| XANPAGTX0501_003775-T2 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.015597 |
| XANPAGTX0501_004104-T1 | IPR001214 | IPR | SET domain | Cell division, proliferation and growth | Fungal multicellularity | -1.419256 |
| XANPAGTX0501_004628-T1 | IPR012337 | IPR | Ribonuclease H-like superfamily | Cell division, proliferation and growth | Fungal multicellularity | -1.317480 |
| XANPAGTX0501_003124-T1 | IPR001461 | IPR | Aspartic peptidase A1 family | Cell surface and cell wall proteins | Fungal multicellularity | -1.035285 |
| XANPAGTX0501_005735-T1 | IPR018824 | IPR | Conidiation-specific protein 6 | Cell surface and cell wall proteins | Fungal multicellularity | -1.620055 |
| XANPAGTX0501_006327-T1 | IPR018466 | IPR | Yeast cell wall synthesis Kre9/Knh1-like, N-terminal | Cell wall biosynthesis | Fungal multicellularity | -1.922253 |
| XANPAGTX0501_001856-T1 | IPR037176 | IPR | Osmotin/thaumatin-like superfamily | Cell wall remodeling | Fungal multicellularity | -1.894636 |
| XANPAGTX0501_007833-T1 | IPR002889 | IPR | Carbohydrate-binding WSC | Cell wall remodeling | Fungal multicellularity | -1.003237 |
| XANPAGTX0501_009511-T1 | GH16 | CAZy | act on beta-1,4 or beta-1,3 glycosidic bonds in glucans and galactans | Cell wall remodeling | Fungal multicellularity | -1.136478 |
| XANPAGTX0501_001064-T1 | IPR021765 | IPR | Mycotoxin biosynthesis protein UstYa-like | Defense | Fungal multicellularity | -1.234644 |
| XANPAGTX0501_001643-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.215746 |
| XANPAGTX0501_003212-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.384927 |
| XANPAGTX0501_003213-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.399730 |
| XANPAGTX0501_005620-T1 | IPR017907 | IPR | Zinc finger; RING-type; conserved site | Protein ubiquitination | Fungal multicellularity | -1.188513 |
| XANPAGTX0501_005815-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.064277 |
| XANPAGTX0501_006203-T1 | IPR017907 | IPR | Zinc finger; RING-type; conserved site | Protein ubiquitination | Fungal multicellularity | -1.175049 |
| XANPAGTX0501_007869-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.136332 |
| XANPAGTX0501_008856-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.339511 |
| XANPAGTX0501_009316-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.246011 |
| XANPAGTX0501_009942-T1 | IPR001810 | IPR | F-box domain | Protein ubiquitination | Fungal multicellularity | -1.164912 |
| XANPAGTX0501_010380-T1 | IPR000210 | IPR | BTB/POZ domain | Protein ubiquitination | Fungal multicellularity | -1.223224 |
| XANPAGTX0501_002098-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.056175 |
| XANPAGTX0501_002123-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.092697 |
| XANPAGTX0501_004217-T1 | IPR000504 | IPR | RNA recognition motif domain | RNA binding proteins | Expression regulation | -1.376777 |
| XANPAGTX0501_002123-T1 | IPR007855 | IPR | RNA-dependent RNA polymerase, eukaryotic-type | RNA interference | Expression regulation | -1.092697 |
| XANPAGTX0501_003775-T1 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.352148 |
| XANPAGTX0501_003775-T2 | IPR032474 | IPR | Protein argonaute, N-terminal | RNA interference | Expression regulation | -1.015597 |
| XANPAGTX0501_000420-T1 | IPR013087 | IPR | Zinc finger C2H2-type | Transcription factors | Expression regulation | -1.104047 |
| XANPAGTX0501_001955-T1 | IPR036864 | IPR | Zn(2)-C6 fungal-type DNA-binding domain superfamily | Transcription factors | Expression regulation | -1.028447 |
| XANPAGTX0501_001958-T1 | IPR001356 | IPR | Homeobox domain | Transcription factors | Expression regulation | -1.511188 |
| XANPAGTX0501_005620-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.188513 |
| XANPAGTX0501_006203-T1 | IPR013083 | IPR | Zinc finger, RING/FYVE/PHD-type | Transcription factors | Expression regulation | -1.175049 |
| XANPAGTX0501_001825-T1 | IPR036259 | IPR | MFS transporter superfamily | Transporters | Fungal multicellularity | -1.063406 |
###enrichment analysis
enrich<-clusterProfiler::enricher(ap_a_genes$target_id,
pAdjustMethod = "none",
minGSSize = 1,
maxGSSize = 2000,
qvalueCutoff = 1,
universe=ips_data$universe,
TERM2GENE=ips_data$term2protein,
TERM2NAME=ips_data$term2name)
enrich_pairwise<-enrichplot::pairwise_termsim(enrich)
enrichplot::emapplot(enrich_pairwise)
pdf(file="../results/apothecia_upr.pdf",width=6,height=5)
enrichplot::emapplot(enrich_pairwise,cex_label_category=0.4,cex_line=0.25,
shadowtext=F,cex_pie2axis=0.1,repel=T)
dev.off()
## quartz_off_screen
## 2
venn_a2<-list(compared_to_center = ca_sig$target_id[ca_sig$change=="apothecium"],
compared_to_edge = ea_sig$target_id[ea_sig$change=="apothecium"],
compared_to_center_edge_pooled=a_sig$target_id[a_sig$change=="apothecium"])
a2<-ggVennDiagram(venn_a2,label_size = 5,set_size=5)+labs(title = "Upregulated in apothecia")+theme(title=element_text(size=12))+scale_x_continuous(expand = expansion(mult = .4))
a2
library(ComplexHeatmap)
library(viridis)
#make a matrix
tabd_df_a <- a_so$obs_norm[a_so$obs_norm$target_id %in% target_id,]
tabd_df_a <- dplyr::select(tabd_df_a, target_id, sample,
tpm)
tabd_df_a <- reshape2::dcast(tabd_df_a, target_id ~ sample,
value.var = "tpm")
rownames(tabd_df_a) <- tabd_df_a$target_id
tabd_df_a$target_id <- NULL
trans_mat_a <- as.matrix(log(tabd_df_a + 1))
#make a top annotation
#define column annotations
s2c_a <- a_so$sample_to_covariates
s2c_a<-data.frame("sample"= colnames(tabd_df_a)) %>% left_join(s2c_a)
rownames(s2c_a)<-s2c_a$sample
s2c_a<-s2c_a %>% select(part)
ta_colors_a = c("apothecia" = "#619CFF", "thallus_edge" = "#F8766D","thallus_centre"="green")
ta_a = HeatmapAnnotation(df=s2c_a,col = list(condition = ta_colors_a))
#filter to include only MAT locus
filt_mat_MAT<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_002103-T1","XANPAGTX0501_002104-T1"))
HM_mat = Heatmap(filt_mat_MAT, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)
pdf(file="../results/MAT_heatmap.pdf",width=10,height=2)
draw(HM_mat)
dev.off()
## quartz_off_screen
## 2
HM_mat
* lolipop plot arranged by specimen
df<-data.frame(filt_mat_MAT) %>% mutate(target_id=rownames(filt_mat_MAT)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
write.table(df, file="../analysis_and_temp_files/09_dge_architecture/mat_expression.txt", quote=F, sep='\t', row.names=F)
#only include thalli that a. have apothecia sample and b. have at least two samples
incl<-a_so$sample_to_covariates %>% mutate(if_apothecia=ifelse(part=="apothecia",T,F)) %>%
group_by(thallus) %>% summarize(n=n(),n_ap=sum(if_apothecia)) %>% filter(n>1,n_ap>0)
gg<-ggplot(df %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position="bottom")
ggsave('../results/MAT_lopipop.pdf',gg, width = 4, height = 3)
gg
filt_mat_sin3<-subset(trans_mat_a, rownames(trans_mat_a) %in% c("XANPAGTX0501_001156-T1","XANPAGTX0501_001156-T2","XANPAGTX0501_001156-T3"))
HM_sin3 = Heatmap(filt_mat_sin3, show_row_names = T, show_column_names = T,cluster_rows = T, row_title_rot = 0, col=viridis(100), heatmap_legend_param = list(title = "Expression: log(TPM)"), top_annotation = ta_a)
draw(HM_sin3)
df_sin3<-data.frame(filt_mat_sin3) %>% mutate(target_id=rownames(filt_mat_sin3)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
ggplot(df_sin3 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
scale_color_manual( values = color_scheme)+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))
This is very interesting, but also inconsistent. Looked at the bam file but it didn’t clarify much
Visualize several key gene for the suppl. figure
library(patchwork)
ap_genes<-c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1","XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1")
filt_mat_ap<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes)
df_ap<-data.frame(filt_mat_ap) %>% mutate(target_id=rownames(filt_mat_ap)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap$target_id<-factor(df_ap$target_id,levels=c("XANPAGTX0501_004521-T1","XANPAGTX0501_001958-T1","XANPAGTX0501_004580-T1","XANPAGTX0501_005735-T1","XANPAGTX0501_002123-T1","XANPAGTX0501_003775-T1","XANPAGTX0501_004244-T1",
"XANPAGTX0501_004217-T1", "XANPAGTX0501_002098-T1") )
gg_ap<-ggplot(df_ap %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45))+
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6))
ap_genes2<-c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
"XANPAGTX0501_010380-T1")
filt_mat_ap2<-subset(trans_mat_a, rownames(trans_mat_a) %in% ap_genes2)
df_ap2<-data.frame(filt_mat_ap2) %>% mutate(target_id=rownames(filt_mat_ap2)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
df_ap2$target_id<-factor(df_ap2$target_id,levels=c("XANPAGTX0501_003213-T1", "XANPAGTX0501_008856-T1", "XANPAGTX0501_009316-T1","XANPAGTX0501_009942-T1", "XANPAGTX0501_003212-T1", "XANPAGTX0501_001643-T1","XANPAGTX0501_005815-T1","XANPAGTX0501_007869-T1",
"XANPAGTX0501_010380-T1") )
gg_ap2<-ggplot(df_ap2 %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6))
gg_ap_all<-gg_ap+gg_ap2+ plot_layout(axis_titles = "collect",guides = 'collect')
ggsave('../results/apothecia_dge_lopipop.pdf',gg_ap_all, width = 8, height = 10)
#get the matrix for all samples, including culture
tabd_df<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/norm_counts_sleuth.txt")
rownames(tabd_df) <- tabd_df$target_id
tabd_df$target_id <- NULL
tabd_df <- mutate_all(tabd_df, function(x) as.numeric(as.character(x)))
trans_mat_08 <- as.matrix(log(tabd_df + 1))
selected_genes<-c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
df_thalli$target_id<-factor(df_thalli$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
axis.text.x = element_blank(),axis.ticks.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
df_culture$target_id<-factor(df_culture$target_id,levels=c("XANPAGTX0501_008856-T1","XANPAGTX0501_002123-T1"))
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
axis.ticks = element_blank(),
axis.title.y = element_blank() )
ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 2.5))
#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_003775-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
strip.background.x = element_blank(),strip.text.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.y = element_blank() )
ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))
sel_final<-ggsel/plot_spacer()/ggsel2+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.66,-0.155,0.34)) &theme(legend.position = "bottom")
ggsave('../results/selected_apothecia_dge_lopipop.pdf',sel_final, width = 7, height = 4)
sel_final
#get the matrix for all samples, including culture
selected_genes<-c("XANPAGTX0501_009376-T1","XANPAGTX0501_008852-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
strip.background.x = element_blank(),strip.text.x = element_blank())
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.y = element_blank() )
ggsel<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 5))
#had to make one of them separately baceaus of the axes issue
selected_genes<-c("XANPAGTX0501_001015-T1")
selected_genes<-c("XANPAGTX0501_001643-T1")
#graph for the lichen samples
filt_mat_selected_thalli<-subset(trans_mat_a, rownames(trans_mat_a) %in% selected_genes)
df_thalli<-data.frame(filt_mat_selected_thalli) %>% mutate(target_id=rownames(filt_mat_selected_thalli)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>% left_join(a_so$sample_to_covariates)
## Joining with `by = join_by(sample)`
gg_selected_thalli<-ggplot(df_thalli %>% filter(thallus %in% incl$thallus), aes(color=part,y=expression,x=part))+
geom_segment( aes(x=part, xend=part, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~thallus)+
xlab("")+ylab("Expression: log(TPM)")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) +
scale_color_manual( values = color_scheme)+
theme(text=element_text(size=6),legend.position = "bottom",
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.x = element_blank() )
#graph for the culture
filt_mat_selected_culture<-subset(trans_mat_08, rownames(trans_mat_08) %in% selected_genes)
df_culture<-data.frame(filt_mat_selected_culture) %>% mutate(target_id=rownames(filt_mat_selected_culture)) %>%
pivot_longer(-target_id,names_to="sample",values_to="expression") %>%
filter(!(sample %in% colnames(filt_mat_selected_thalli)))
#df_thalli$target_id<-factor(df_selected$target_id,levels=c())
gg_selected_culture<-ggplot(df_culture, aes(y=expression,x=sample))+
geom_segment( aes(x=sample, xend=sample, y=0, yend=expression))+
geom_point(stat = "identity",position=position_dodge(width = .5))+
facet_grid(target_id~.)+
xlab("")+ylab("")+
theme_bw()+ scale_x_discrete(guide = guide_axis(angle = 45)) + theme(text=element_text(size=6),axis.text = element_blank(),
axis.ticks = element_blank(),
axis.title = element_blank() )
ggsel2<-gg_selected_thalli + gg_selected_culture + plot_layout(widths = c(0.6,0.4),nrow = 1) & scale_y_continuous(limits = c(0, 7))
sel_final<-ggsel2/plot_spacer()/ggsel+ plot_layout(axis_titles = "collect",guides = "collect",heights = c(0.34,-0.105,0.66)) &theme(legend.position = "bottom")
ggsave('../results/selected_edge_dge_lopipop.pdf',sel_final, width = 7, height = 4)
sel_final
ec_sig$Comparison<-"Edge / Center"
ea_sig$Comparison<-"Edge / Apothecia"
ca_sig$Comparison<-"Center / Apothecia"
a_sig$Comparison<-"Apothecia / Vegetative (edge + center)"
compiled<-rbind(ec_sig,ea_sig,ca_sig,a_sig) %>% filter(change!="low_logFC") %>%
left_join(funannot2,by=c("target_id"="TranscriptID")) %>%
select(Comparison,change,target_id,b,InterPro_new,CAZyme_new,Protease_new,KO,secreted_consensus,lichen_ortho) %>% arrange(change) %>% arrange(Comparison)
write.table(compiled, file="../results/tissue_dge.txt", quote=F, sep='\t', row.names=F)
apothecia_up<-compiled$target_id[compiled$change=="apothecium"]
center_up<-ec_sig$target_id[ec_sig$change=="centre"]
ec_sig %>% filter(change=="centre") %>%
mutate(apothecia_upregulated = ifelse(target_id %in%apothecia_up,T,F)) %>%
select(target_id,apothecia_upregulated,b)
## # A tibble: 9 × 3
## target_id apothecia_upregulated b
## <chr> <lgl> <dbl>
## 1 XANPAGTX0501_005615-T1 TRUE -1.01
## 2 XANPAGTX0501_005614-T1 TRUE -1.08
## 3 XANPAGTX0501_008007-T1 TRUE -1.16
## 4 XANPAGTX0501_002184-T1 TRUE -1.17
## 5 XANPAGTX0501_001949-T1 TRUE -1.19
## 6 XANPAGTX0501_002506-T1 TRUE -1.19
## 7 XANPAGTX0501_008856-T1 TRUE -1.28
## 8 XANPAGTX0501_009886-T1 TRUE -1.29
## 9 XANPAGTX0501_009927-T1 TRUE -1.62
compiled %>% filter(change=="apothecium", target_id %in% center_up) %>%
select(target_id,Comparison) %>% mutate(presence=1) %>%
pivot_wider(names_from = Comparison,values_from = presence, values_fill=0)
## # A tibble: 9 × 4
## target_id Apothecia / Vegetati…¹ `Center / Apothecia` `Edge / Apothecia`
## <chr> <dbl> <dbl> <dbl>
## 1 XANPAGTX0501_0… 1 0 1
## 2 XANPAGTX0501_0… 1 1 1
## 3 XANPAGTX0501_0… 1 0 1
## 4 XANPAGTX0501_0… 1 1 1
## 5 XANPAGTX0501_0… 1 1 1
## 6 XANPAGTX0501_0… 1 1 1
## 7 XANPAGTX0501_0… 0 0 1
## 8 XANPAGTX0501_0… 0 0 1
## 9 XANPAGTX0501_0… 0 0 1
## # ℹ abbreviated name: ¹`Apothecia / Vegetative (edge + center)`
lichen_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_lichen_sleuth.txt")
count_function<-ips_selected %>% filter(TranscriptID %in%lichen_upr$target_id) %>% group_by(Function) %>% summarize(total=n())
ips_selected %>% filter(TranscriptID %in% lichen_upr$target_id) %>%
mutate(is_ap = ifelse(TranscriptID %in% apothecia_up,T,F)) %>%
group_by(Function) %>% summarize(in_apothecia_up=sum(is_ap)) %>% left_join(count_function)
## Joining with `by = join_by(Function)`
## # A tibble: 19 × 3
## Function in_apothecia_up total
## <chr> <int> <int>
## 1 "Acetyl-CoA production and metabolism" 1 4
## 2 "Carbohydrate storage" 1 1
## 3 "Cell division, proliferation and growth" 6 12
## 4 "Cell surface and cell wall proteins" 2 9
## 5 "Cell wall biosynthesis " 1 1
## 6 "Cell wall misc" 0 2
## 7 "Cell wall remodeling" 1 3
## 8 "Defense" 1 3
## 9 "G-proteins and GPCR" 0 1
## 10 "Lipid metabolism" 0 3
## 11 "Oxylipins" 0 2
## 12 "Protein ubiquitination" 8 14
## 13 "RNA binding proteins" 4 5
## 14 "RNA interference" 3 3
## 15 "Ribosomal genes" 0 1
## 16 "Stress response genes" 0 1
## 17 "Transcription factors" 5 23
## 18 "Transporters" 0 27
## 19 "Velvet" 0 2
compiled %>% filter(change=="apothecium", grepl("transporter",InterPro_new)) %>%
filter(InterPro_new!="IPR004853 Sugar phosphate transporter domain",
!grepl("ABC transporter-like",InterPro_new)) %>%
select(target_id,InterPro_new,b,Comparison) %>%
mutate(lichen_upregulated = ifelse(target_id %in%lichen_upr$target_id,T,F))
## # A tibble: 7 × 5
## target_id InterPro_new b Comparison lichen_upregulated
## <chr> <chr> <dbl> <chr> <lgl>
## 1 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.06 Apothecia… FALSE
## 2 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.16 Apothecia… TRUE
## 3 XANPAGTX0501_008594-T1 IPR036259 MFS tran… -1.04 Edge / Ap… FALSE
## 4 XANPAGTX0501_000281-T1 IPR011701 Major fa… -1.28 Edge / Ap… FALSE
## 5 XANPAGTX0501_001825-T1 IPR003663 Sugar/in… -1.40 Edge / Ap… FALSE
## 6 XANPAGTX0501_009737-T1 IPR005829 Sugar tr… -1.54 Edge / Ap… FALSE
## 7 XANPAGTX0501_010381-T1 IPR002293 Amino ac… -1.59 Edge / Ap… TRUE
culture_upr<-read.delim2("../analysis_and_temp_files/08_dge_culture_lichen/upreg_in_culture_sleuth.txt")
compiled %>% mutate(lichen_cult = case_when(
target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
target_id %in% culture_upr$target_id ~ "upreg_culture",
T ~ "non_dge"
)) %>% group_by(Comparison,change,lichen_cult) %>%
summarize(n=n()) %>%
pivot_wider(names_from=lichen_cult,values_from = n,values_fill = 0) %>%
mutate(total= upreg_lichen+upreg_culture+non_dge)
## `summarise()` has grouped output by 'Comparison', 'change'. You can override
## using the `.groups` argument.
## # A tibble: 7 × 6
## # Groups: Comparison, change [7]
## Comparison change non_dge upreg_culture upreg_lichen total
## <chr> <chr> <int> <int> <int> <int>
## 1 Apothecia / Vegetative (edge … apoth… 56 17 177 250
## 2 Apothecia / Vegetative (edge … thall… 0 1 1 2
## 3 Center / Apothecia apoth… 21 7 90 118
## 4 Center / Apothecia centre 0 0 1 1
## 5 Edge / Apothecia apoth… 121 25 225 371
## 6 Edge / Apothecia edge 3 1 9 13
## 7 Edge / Center centre 1 1 7 9
compiled2 <- compiled %>% mutate(lichen_cult = case_when(
target_id %in% lichen_upr$target_id ~ "upreg_lichen" ,
target_id %in% culture_upr$target_id ~ "upreg_culture",
T ~ "non_dge")) %>%
filter(lichen_cult=="upreg_culture")
compiled2 %>% kable(format = "html", col.names = colnames(compiled2)) %>%
kable_styling() %>%
kableExtra::scroll_box(width = "100%", height = "400px")
| Comparison | change | target_id | b | InterPro_new | CAZyme_new | Protease_new | KO | secreted_consensus | lichen_ortho | lichen_cult |
|---|---|---|---|---|---|---|---|---|---|---|
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_007473-T1 | -1.021407 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001223-T1 | -1.064214 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_009599-T1 | -1.070929 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001948-T1 | -1.099351 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_006310-T1 | -1.105045 | IPR022137 Zinc finger protein, DUF3669 domain | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001643-T1 | -1.215746 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001952-T1 | -1.257146 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001950-T1 | -1.259001 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001951-T1 | -1.262779 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_001947-T1 | -1.303157 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_002165-T1 | -1.325802 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_002163-T1 | -1.392989 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_002164-T1 | -1.582652 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_009619-T1 | -1.640066 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_003209-T1 | -1.709229 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_009602-T1 | -1.777131 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Apothecia / Vegetative (edge + center) | apothecium | XANPAGTX0501_008109-T1 | -2.159140 | IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain | NA | NA | K03800 | FALSE | FALSE | upreg_culture |
| Apothecia / Vegetative (edge + center) | thallus | XANPAGTX0501_009376-T1 | 2.496154 | IPR043141 Ribosomal protein L10-like domain superfamily | NA | NA | K02864 | FALSE | FALSE | upreg_culture |
| Center / Apothecia | apothecium | XANPAGTX0501_002163-T1 | -1.035184 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_001947-T1 | -1.046488 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_001951-T1 | -1.118810 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_003209-T1 | -1.170208 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_009602-T1 | -1.212068 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_009619-T1 | -1.314627 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Center / Apothecia | apothecium | XANPAGTX0501_008109-T1 | -2.657633 | IPR004143 Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain | NA | NA | K03800 | FALSE | FALSE | upreg_culture |
| Edge / Apothecia | apothecium | XANPAGTX0501_005583-T1 | -1.079779 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_000885-T1 | -1.108859 | IPR036305 RGS domain superfamily | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_010011-T1 | -1.134493 | IPR036013 Band 7/SPFH domain superfamily | NA | NA | K07192 | FALSE | FALSE | upreg_culture |
| Edge / Apothecia | apothecium | XANPAGTX0501_009812-T1 | -1.143459 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009785-T1 | -1.191020 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009599-T1 | -1.242828 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_003864-T1 | -1.363940 | IPR009075 Acyl-CoA dehydrogenase/oxidase C-terminal, IPR009100 Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily, IPR013786 Acyl-CoA dehydrogenase/oxidase, N-terminal, IPR036250 Acyl-CoA dehydrogenase-like, C-terminal, IPR037069 Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_007473-T1 | -1.375934 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_007936-T1 | -1.379176 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_005640-T1 | -1.380432 | IPR013087 Zinc finger C2H2-type | NA | NA | FALSE | TRUE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009761-T1 | -1.387848 | IPR001283 Cysteine-rich secretory protein-related, IPR014044 CAP domain, IPR018244 Allergen V5/Tpx-1-related, conserved site, IPR034120 None, IPR035940 CAP superfamily | NA | NA | K20412 | TRUE | FALSE | upreg_culture |
| Edge / Apothecia | apothecium | XANPAGTX0501_001951-T1 | -1.498238 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009737-T1 | -1.540774 | IPR005829 Sugar transporter, conserved site, IPR011701 Major facilitator superfamily, IPR020846 Major facilitator superfamily domain, IPR036259 MFS transporter superfamily | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001948-T1 | -1.662753 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001950-T1 | -1.678963 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001949-T1 | -1.732732 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001947-T1 | -1.767840 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_002163-T1 | -1.904022 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001643-T1 | -1.910689 | IPR001810 F-box domain, IPR032675 Leucine-rich repeat domain superfamily, IPR036047 F-box-like domain superfamily | NA | NA | FALSE | TRUE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_002165-T1 | -1.959472 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_001952-T1 | -2.002699 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009619-T1 | -2.203533 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_003209-T1 | -2.437600 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_009602-T1 | -2.500879 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | apothecium | XANPAGTX0501_002164-T1 | -2.527734 | NA | NA | NA | FALSE | FALSE | upreg_culture | |
| Edge / Apothecia | edge | XANPAGTX0501_006869-T1 | 1.099929 | IPR008979 Galactose-binding-like domain superfamily, IPR017853 Glycoside hydrolase superfamily, IPR024655 Asl1-like, glycosyl hydrolase catalytic domain | GH128 | NA | TRUE | FALSE | upreg_culture | |
| Edge / Center | centre | XANPAGTX0501_001949-T1 | -1.187615 | NA | NA | NA | FALSE | FALSE | upreg_culture |